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TBC1D16 Gene

protein-coding   GIFtS: 47
GCID: GC17M077907

TBC1 Domain Family, Member 16

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
TBC1 Domain Family, Member 161 2
TBC1 Domain Family Member 162

External Ids:    HGNC: 283561   Entrez Gene: 1250582   Ensembl: ENSG000001672917   UniProtKB: Q8TBP03   

Export aliases for TBC1D16 gene to outside databases

Previous GC identifers: GC17M078609 GC17M078611 GC17M075513 GC17M077913 GC17M073354


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for TBC1D16 Gene:
TBC1D16 (TBC1 domain family, member 16) is a protein-coding gene. GO annotations related to this gene include Rab GTPase activator activity. An important paralog of this gene is SGSM1.

UniProtKB/Swiss-Prot: TBC16_HUMAN, Q8TBP0
Function: May act as a GTPase-activating protein for Rab family protein(s)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000017.10  NT_010783.16  NC_018928.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the TBC1D16 gene promoter:
         SREBP-1c   AP-2gamma   GATA-1   SREBP-1b   RORalpha1   SREBP-1a   AP-2beta   AP-2alpha   MRF-2   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTBC1D16 promoter sequence
   Search Chromatin IP Primers for TBC1D16

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TBC1D16


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17q25.3   Ensembl cytogenetic band:  17q25.3   HGNC cytogenetic band: 17q25.3

TBC1D16 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TBC1D16 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M077907:  view genomic region     (about GC identifiers)

Start:
77,906,142 bp from pter      End:
78,009,647 bp from pter
Size:
103,506 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: TBC16_HUMAN, Q8TBP0 (See protein sequence)
Recommended Name: TBC1 domain family member 16  
Size: 767 amino acids; 86372 Da

Explore the universe of human proteins at neXtProt for TBC1D16: NX_Q8TBP0

Explore proteomics data for TBC1D16 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See TBC1D16 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001258773.1  NP_001258774.1  NP_001258775.1  NP_061893.2  

    ENSEMBL proteins: 
     ENSP00000309794   ENSP00000461522   ENSP00000341517   ENSP00000458766   ENSP00000458377  
     ENSP00000461531   ENSP00000461509   ENSP00000458356   ENSP00000459342  

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    Cloud-Clone Corp. Proteins for TBC1D16

     
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    antibodies-online proteins for TBC1D16 (3 products) 

     
    antibodies-online peptides for TBC1D16

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    antibodies-online antibodies for TBC1D16 (8 products) 

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR000195 Rab-GTPase-TBC_dom

    Graphical View of Domain Structure for InterPro Entry Q8TBP0

    ProtoNet protein and cluster: Q8TBP0

    1 Blocks protein domain: IPB000195 RabGAP/TBC domain

    UniProtKB/Swiss-Prot: TBC16_HUMAN, Q8TBP0
    Similarity: Contains 1 Rab-GAP TBC domain


    Find genes that share domains with TBC1D16           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TBC16_HUMAN, Q8TBP0
    Function: May act as a GTPase-activating protein for Rab family protein(s)

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005097Rab GTPase activator activity IEA--
         
    Find genes that share ontologies with TBC1D16           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for TBC1D16

    miRNA
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    miRTarBase miRNAs that target TBC1D16:
    hsa-mir-26a-5p (MIRT050161)

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    SwitchGear 3'UTR luciferase reporter plasmidTBC1D16 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus2
    cytosol1
    endoplasmic reticulum1
    mitochondrion1

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TBC1D16
    Interactions:

        Search GeneGlobe Interaction Network for TBC1D16

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for TBC1D16 (ENSP000003097944) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GABARAPL1ENSP000002664584STRING: ENSP00000266458
    MAP1LC3AENSP000003639704STRING: ENSP00000363970
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0032313regulation of Rab GTPase activity ----

    Find genes that share ontologies with TBC1D16           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for TBC1D16 (TBC16)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for TBC1D16 gene (4 alternative transcripts): 
    NM_001271844.1  NM_001271845.1  NM_001271846.1  NM_019020.3  

    Unigene Cluster for TBC1D16:

    TBC1 domain family, member 16
    Hs.369819  [show with all ESTs]
    Unigene Representative Sequence: NM_019020
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000310924(uc002jxj.3) ENST00000576768(uc002jxi.3) ENST00000340848(uc002jxh.3)
    ENST00000572862(uc002jxk.1) ENST00000570373 ENST00000574241 ENST00000573782
    ENST00000574427 ENST00000571872
    miRNA
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    Inhib. RNA
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat TBC1D16
      QuantiTect SYBR Green Assays in human, mouse, rat TBC1D16
      QuantiFast Probe-based Assays in human, mouse, rat TBC1D16

    Additional mRNA sequence: 

    AB449902.1 AK000755.1 AK091923.1 AK097283.1 AL157485.1 AL512709.1 BC001525.2 BC028290.1 
    BC036947.1 BC062601.1 BC080571.1 CR936670.1 

    18 DOTS entries:

    DT.211671  DT.437983  DT.91923186  DT.115081  DT.92421069  DT.100786813  DT.95282864  DT.95342182 
    DT.40122379  DT.100786818  DT.120978682  DT.120978692  DT.120978698  DT.120978700  DT.75140612  DT.91879936 
    DT.95099692  DT.99941161 

    Selected AceView cDNA sequences (see all 306):

    AI990892 BM451213 AW501834 BX108289 AI264271 AI815027 BU732601 BQ009514 
    BC062601 BG574260 BG576098 BQ182969 BG820848 BE327852 BG762541 BM695082 
    BQ899284 BI862132 NM_019020 BU931938 AI554045 CB217153 BQ689412 BE277141 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for TBC1D16 (see all 8)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16a · 16b
    SP1:                                -                 -     -                                               -                     
    SP2:                                                        -                                               -                     
    SP3:                                                        -                                                                     
    SP4:                                                        -                                                                     
    SP5:                                                                                                                              


    ECgene alternative splicing isoforms for TBC1D16

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    TBC1D16 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GATTCCACAG
    TBC1D16 Expression
    About this image

    TBC1D16 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TBC1D16 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.369819
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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for TBC1D16 gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tbc1d161 , 5 TBC1 domain family, member 161, 5 84.73(n)1
    88.77(a)1
      11 (83.34 cM)5
    2075921  NM_172443.31  NP_766031.21 
     1191430455 
    chicken
    (Gallus gallus)
    Aves TBC1D161 TBC1 domain family, member 16 77.41(n)
    78.95(a)
      768712  XM_004946284.1  XP_004946341.1 
    lizard
    (Anolis carolinensis)
    Reptilia TBC1D166
    TBC1 domain family, member 16
    76(a)
    1 ↔ 1
    2(100679494-100726963)
    African clawed frog
    (Xenopus laevis)
    Amphibia MGC688832 hypothetical protein MGC68883 76.55(n)    BC057720.1 
    zebrafish
    (Danio rerio)
    Actinopterygii tbc1d161 TBC1 domain family, member 16 72.37(n)
    74.89(a)
      450056  NM_001006076.2  NP_001006076.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG53371 CG5337 56.51(n)
    48.35(a)
      34431  NM_135559.3  NP_609403.2 
    worm
    (Caenorhabditis elegans)
    Secernentea tbc-161 tbc-16 50.03(n)
    46.52(a)
      180856  NM_076587.4  NP_508988.3 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes GYP76
    GTPase-activating protein for yeast Rab family mem...
    17(a)
    1 → many
    IV(34237-36477) YDL234C


    ENSEMBL Gene Tree for TBC1D16 (if available)
    TreeFam Gene Tree for TBC1D16 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TBC1D16 gene
    SGSM12  TBC1D172  SGSM22  TBC1D152  TBC1D252  
    5 SIMAP similar genes for TBC1D16 using alignment to 11 protein entries:     TBC16_HUMAN (see all proteins):
    DKFZp761D0223    TBC1D15    TBC1D25    TBC1D17    OATL1

    Find genes that share paralogs with TBC1D16           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for TBC1D16 (see all 2438)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1435950251,2
    C--77905786(+) AAAGC-/AGAGGCT 3 -- int10--------
    rs740017861,2
    C,F--77905824(+) AAGCCG/TCACCC 3 -- int15Minor allele frequency- T:0.10WA CSA NA EA 362
    rs1174111001,2
    C,F--77905912(+) GCAGCG/AGCTCT 3 -- int11Minor allele frequency- A:0.06EA 120
    rs1145725581,2
    F--77905947(+) CAAGAG/ACACGC 3 -- int11Minor allele frequency- A:0.02WA 118
    rs126003591,2
    C,F,A,H--77905950(+) GAGCAC/TGCACT 3 -- int112Minor allele frequency- T:0.26NA CSA WA EA 378
    rs1840265011,2
    --77905958(+) ACTCAA/GAACCC 3 -- int10--------
    rs1506402391,2
    C--77906032(+) AGCCCA/GCCCCG 3 -- int10--------
    rs1879660141,2
    --77906094(+) GAAAAG/TTGGAG 3 -- int10--------
    rs72152381,2
    C,F,H--77906124(+) CTCCAA/TTAATC 3 -- int111Minor allele frequency- T:0.45NA WA CSA EA 377
    rs1810193881,2
    --77906169(+) TTTATG/TTTAAA 3 -- ut310--------

    HapMap Linkage Disequilibrium report for TBC1D16 (77906142 - 78009647 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for TBC1D16 (see all 19):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2666144CNV Deletion23128226
    dgv572e199CNV Deletion23128226
    esv2671544CNV Deletion23128226
    esv2716355CNV Deletion23290073
    esv2716354CNV Deletion23290073
    esv2716353CNV Deletion23290073
    esv2210925CNV Deletion18987734
    esv2642422CNV Insertion19546169
    nsv527410CNV Loss19592680
    dgv3295n71CNV Loss21882294

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    Find genes that share disorders with TBC1D16           About GenesLikeMe

    Genetic Association Database (GAD): TBC1D16

    Export disorders for TBC1D16 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for TBC1D16 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with TBC1D16)
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    1. TBC1D16 is a Rab4A GTPase activating protein that regulates receptor recycling and EGF receptor signaling. (PubMed id 23019362)1, 3 Goueli B.S....Pfeffer S.R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. Rab GTPase-activating proteins in autophagy: regulation of endocytic and autophagy pathways by direct binding to human ATG8 modifiers. (PubMed id 22354992)1 Popovic D....Dikic I. (Mol. Cell. Biol. 2012)
    4. An integrated approach to uncover drivers of cancer. (PubMed id 21129771)1 Akavia U.D....Pe'er D. (Cell 2010)
    5. Identification and characterization of a novel Tre-2/Bub2/Cdc16 (TBC) protein that possesses Rab3A-GAP activity. (PubMed id 19077034)1 Ishibashi K.... Fukuda M. (Genes Cells 2009)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    7. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. (PubMed id 15146197)1 Brandenberger R.... Stanton L.W. (Nat. Biotechnol. 2004)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 125058 HGNC: 28356 AceView: TBC1D16 Ensembl:ENSG00000167291 euGenes: HUgn125058
    ECgene: TBC1D16 H-InvDB: TBC1D16

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for TBC1D16 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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